## [1] "Max fold diff lib size = 1.75956241223834"
## [1] "57820 total transcripts. Keeping 17782 transcripts after filtering"
Heirarchical clustering based on expression profile Spearman correlations. This shows that the data are overall high quality (no outliers), with good grouping of samples within-cell lines. The biggest difference is clearly between colon and ovarian cell lines.
Comparing distribution of log-counts per million per sample looks reasonable
Collapse replicates
Save LCPM data (rep collapsed)
Collapse across replicates by summing read counts Model cell line as random effect
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## [1] "Running gene-permutation testing with 100000 perms"
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Estimated KO effect in Dependent - Independent lines
## [1] "Running gene-permutation testing with 100000 perms"
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